# HG changeset patch
# User luca_milaz
# Date 1728895852 0
# Node ID a78d83753ccec809e5537db85af5db6bf6e127e6
# Parent  d40d5d5435df7b47a1b9ddd387d84ec8de593ca0
Uploaded

diff -r d40d5d5435df -r a78d83753cce COBRAxy/ras_to_bounds.xml
--- a/COBRAxy/ras_to_bounds.xml	Mon Oct 14 08:48:54 2024 +0000
+++ b/COBRAxy/ras_to_bounds.xml	Mon Oct 14 08:50:52 2024 +0000
@@ -84,6 +84,7 @@
 This tool generates the reactions bounds for a given metabolic model (JSON or XML format) both with and without the use of the Reaction Activity Scores (RAS) matrix generated by RAS generator.
 Moreover, it enables to use custom/pre-defined growth mediums to constrain exchange reactions. For a custom medium, It is suggested to use the template file returned by the Custom Data Generator tool.
 If the RAS matrix, generated by the RAS generator tool, is used, then a bounds file is generated for each cell. Otherwise, a single bounds file is returned.
+By default, all reactions in model.medium that are not present in the medium file have lower bound set to 0.0 and not set to the default model value.
 
 Accepted files:
     - A model: JSON or XML file reporting reactions and rules contained in the model.